generally its best to use the software plugin with that game, using the hardware plugins along with certain types of texture filtering settings has been known to cause seveal issues, the most common being the black overworld map glitch.
get past the first two battles so you can get to the part where you are able to move around on the world map and find out if this issue has been triggered.
try installing that, some AMD dual core models have performance issues with certain applications, epsxe being one of them. as for your GPU, make sure your drivers are up-to-date, you can try disabling the screen filtering setting as it uses up a bit of your card's memory and can lower the performance on some systems.
you should also enter the amount of video memory manually, the auto detect setting does not work for ATI users, not doing so can also lower performance and i would bet that part of your problem right now is due to it being set to that.
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